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https://github.com/aehrc/pathling

Tools that make it easier to use FHIR® and clinical terminology within data analytics, built on Apache Spark.
https://github.com/aehrc/pathling

analytics fhir spark standards terminology

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Tools that make it easier to use FHIR® and clinical terminology within data analytics, built on Apache Spark.

Host: GitHub
URL: https://github.com/aehrc/pathling
Owner: aehrc
License: apache-2.0
Created: 2020-03-23T05:22:00.000Z (over 4 years ago)
Default Branch: main
Last Pushed: 2024-10-29T05:35:57.000Z (15 days ago)
Last Synced: 2024-10-29T23:33:49.303Z (14 days ago)
Topics: analytics, fhir, spark, standards, terminology
Language: Java
Homepage: https://pathling.csiro.au
Size: 149 MB
Stars: 88
Watchers: 14
Forks: 12
Open Issues: 168
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff

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Pathling is a set of tools that make it easier to

use [FHIR®](https://hl7.org/fhir/R4) and clinical terminology within health

data analytics. It is built on [Apache Spark](https://spark.apache.org), and

includes both language libraries and a server implementation.

[**Read the documentation →**](https://pathling.csiro.au/docs)

    

    

    

    

## What can it do?

### Query and transformation of FHIR data

[FHIR R4](https://hl7.org/fhir/R4) is the dominant standard for exchanging health

data. It comes in both [JSON](https://hl7.org/fhir/json.html)

or [XML](https://hl7.org/fhir/xml.html) formats, and can contain over 140

different types of resources, such

as [Patient](https://hl7.org/fhir/patient.html), 

[Observation](https://hl7.org/fhir/observation.html), 

[Condition](https://hl7.org/fhir/condition.html), 

[Procedure](https://hl7.org/fhir/procedure.html), and many more.

Pathling is capable of reading all the different types of FHIR resources into a

format suitable for data analysis tasks. This makes the following things

possible:

- Querying FHIR data using SQL and [FHIRPath](/docs/fhirpath)

- Transforming data into other formats, such as CSV

  or [Parquet](https://parquet.apache.org/)

- Performing terminology queries against coded fields within the FHIR data

See [Encoders](https://pathling.csiro.au/docs/libraries/encoders) for more information.

### Terminology queries

Health data often contains codes from systems such

as [SNOMED CT](https://www.snomed.org/snomed-ct/five-step-briefing), [LOINC](https://loinc.org/)

or [ICD](https://www.who.int/standards/classifications/classification-of-diseases).

These codes contain a great deal of information about diagnoses, procedures,

observations and many other aspects of a patient's clinical record.

It is common to group these codes based upon their properties, relationships to

other codes, or membership within a pre-defined set. Pathling can automate the

task of calling out to

a [FHIR terminology server](https://hl7.org/fhir/terminology-service.html) to

ask questions about the codes within your data.

Examples of the types of questions that can be answered include:

- Is this SNOMED CT procedure code a type of endoscopy?

- Does this LOINC test result code have an analyte of bilirubin?

- Is this ICD-10 code within the pre-defined list of codes within my cohort

  definition?

See [Terminology functions](https://pathling.csiro.au/docs/libraries/terminology) for more information.

### FHIR analytics API

Pathling also provides a FHIR server implementation, providing a REST API that

can be used to perform analytic queries over FHIR data. This is useful for

powering interactive web and mobile applications that need to be able to

aggregate, group and transform FHIR data.

See [Server](https://pathling.csiro.au/docs/server) for more information.

## Licensing and attribution

Pathling is copyright © 2018-2023, Commonwealth Scientific and Industrial

Research Organisation

(CSIRO) ABN 41 687 119 230. Licensed under

the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).

This means that you are free to use, modify and redistribute the software as

you wish, even for commercial purposes.

If you use this software in your research, please consider citing our paper, 

[Pathling: analytics on FHIR](https://doi.org/10.1186/s13326-022-00277-1).

**Pathling is experimental software, use it at your own risk!** You can get a

full description of the current set of known issues 

[here](https://github.com/aehrc/pathling/issues).